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Recent Patents of Interest in Proteomics: Jul 31, 2008

US Patent 7,405,401. Ion extraction devices, mass spectrometer devices, and methods of selectively extracting ions and performing mass spectrometry. Inventor: John Hoyes. Assignee: Micromass UK (now Waters)
Invention pertains to a method of selectively extracting ions. The steps include providing a supply of ions in a body of gas; generating a ponderomotive ion trapping potential; generating further potentials “to provide an effective potential which prevents ions from being extracted from an extraction region; trapping the ions; and selectively extracting ions of a predetermined mass-to-charge ratio or ion mobility from the extraction region “in which the characteristics of the effective potential which prevent ions from being extracted from the extraction region are caused, at least in part, by the generation of the ponderomotive ion trapping potential,” according to the patent’s abstract.

US Patent 7,405,396. Sample handling mechanisms and methods for mass spectrometry. Inventors: Thomas Cygan; Vincent Tsang; Raymond Burke; Richard Gill; Roy Martin; Timothy Hutchins. Assignee: Applera (now ABI); MDS
Invention pertains to systems for providing sample ions, methods for providing the ions, and sample support handling mechanisms. The support handling mechanism comprises a sample support transfer mechanism portion and a sample support changing mechanism portion. In various embodiments, the sample support handling mechanism facilitates consistent positioning of a sample support for subsequent ion generation by MALDI.

US Patent 7,402,407. Chemically targeted positional identification of post-translationally phorphorylated peptides. Inventors: Gary Hathaway. Assignee: California Institute of Technology
Provided are methods for determining the position of a post-translationally modified amino acid residue or an O-glycosylated amino acid residue in a peptide. Methods for identifying the PTM amino acid residue in a peptide are also described, and kits for practicing such methods are provided.

US Patent 7,402,397. Detecting and profiling molecular complexes. Inventors: Po-Ying Chan-Hui; Sharat Singh; Hossein Salimi-Moosavi; Hasan Tahir; ; Gerald Wallweber; Hrair Kirakosssian; Tracy Matray. Assignee: Monogram BioSciences
Invention pertains to methods for detecting the formation of complexes of molecules, particularly proteins in a sample such as a cell or tissue lysate. In one aspect, a cleaving probe specific for a first protein in a complex and binding compounds specific for one for more second proteins in a complex are provided. The cleaving probe is induced to generate an active series upon binding, cleaving molecular tags attached to the binding compounds in the local region of the cleaving probe. The released molecular tags are separated from the assay mixture and from each other, providing a readout that is related to the number and types of proteins present in the complex.

US Patent 7,399,962. All-mass MS/MS method and apparatus. Inventor: Alexander Makarov. Assignee: Thermo Finnigan (now Thermo Fisher Scientific)
Described is a method for obtaining a mass spectrum of elements in a sample. Sample precursor ions are generated and fragmented at a dissociation site. The fragment ions are then guided onto an ion trap of the electrostatic or “Orbitrap” type. Fragment ions entering onto the trap are in groups dependent on precursor ion m/z with each group’s m/z determined from the axial movement of ions in the trap. The electric field in the trap is distorted. “Ions of the same m/z, that are derived from different pre-cursor ions, are then separated, because the electric field distortion causes the axial movement to become dependent upon factors other than m/z alone,” according to the patent’s abstract.

US Patent 7,399,960. Time of flight mass spectrometer. Inventor: Shinichi Yamaguchi. Assignee: Shimadzu
The instrument described includes an ion source at which an ion starts flying; an energizer for giving a “predetermined amount of energy” to the ion so that it can fly; an ion guide for forming a time-focusing flight path; a detector for detection of the ion after its flight path; an analysis controller; and a mass calculator. The instrument “greatly reduces the time and labor of mass analysis, and a wide range of mass spectrum can be obtained on a scarce sample on which many-time measurements are impossible,” according to the patent’s abstract.

US Patent 7,399,641. Mass spectrometric immunoassay. Inventors: Randall Nelson; Peter Williams; Jennifer Krone. Assignee: Intrinsic Bioprobes
Using affinity capture to isolate analytes and internal reference species and mass spectrometric analysis of the isolated analyte/internal reference species, antibody and antigen analytes are detected and/or quantified. Quantification is done by normalizing and calibrating the obtained mass spectrum against the mass spectrum obtained for an antibody/antigen of known concentration.

US Patent 7,397,026. Efficient electron transfer dissociation for mass spectrometry. Inventor: Jerry Dowell. Assignee: Agilent Technologies
Methods and apparatuses for electron transfer dissociation that vary the internal energy of precursor ions for ETD are described.

US Patent 7,396,688. Mass spectrometric analysis of biopolymers. Inventors: David A. Estell; Grant Ganshaw; Christian Paech; Sigrid Paech. Assignee: Genencor International
The invention makes use of unique tags of a “specific biopolymer that can be exploited for determining the concentration the biopolymer in crude solutions,” according to the patent’s application. In one embodiment, a target biomolecule is chosen for analysis and an analog is generated. Peak area integration of the peptide pairs provides a direct measure for the amount of target protein in the crude solution.

US Patent 7,396,686. Biopolymer sequences by MALDI granddaughter ion spectra. Inventors: Detlev Suckau, Anja Resemann. Assignee: Bruker Daltonik
Invention pertains to the acquisition of spectra of biopolyers, particularly proteins, in MS/MS using MALDI for examining and determining sequence patterns. A method for measuring granddaughter spectra of terminal fragment ions of the biopolymers in MS/MS “wherein a so-called in-source fragmentation to generate a first generation of fragment or daughter ions of a biopolymer is coupled with a subsequent measurement of granddaughter ions, which have been obtained by a further fragmentation of a selected type of daughter ions,” according to the patent’s abstract.

US Patent 7,396,468. Methods and system for protein separation. Inventors: Barry Boyes. Assignee: Agilent Technologies
Invention pertains to membrane proteins and includes fractionating a membrane sample on a reversed-phase superficially porous stationary phase at a temperature greater or equal to 40 degrees Celsius to recover a protein that is more than 70 percent of the mixture of proteins as calculated by weight.

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